[ensembl-dev] Affymetrix Porcine probes: genomic position

[Nathan Johnson]

Hi Dario

We do store array data in the Ensembl Biomart, but this is restricted to the transcript annotations based on the various arrays we cater for, including the Affy porcine array. This is present in the gene mart as an 'External' attribute, but we do not store individual mappings here, just probe/probe_set annotations.

We don't currently provide genome wide array/probe mappings as dumps, primarily because we have had little to no demand for this.  

It would be possible to create these using the API. There is an example script available here which should give you the necessary methods:

	ensembl-functgenomics/scripts/examples/microarray_annotation_example.pl


Thanks

Nath







On 26 Apr 2011, at 13:55, Dario Beraldi wrote:

> Hi Laurent,
> 
> Thanks for taking time to reply. Unfortunately, the file Sus_scrofa.gvf.gz has the probe location for the Illumina Porcine SNP chip. What I'm after is the probe location of the Affymetrix Porcine gene expression array (this one: http://www.affymetrix.com/browse/products.jsp?productId=131488&navMode=34000&navAction=jump&aId=productsNav#1_1).
> 
> I had a look into the subdirectories within ftp://ftp.ensembl.org/pub/release-62/ I but couldn't find anything relevant.
> 
> Any ideas...?
> 
> All the best
> Dario
> 
> Quoting Laurent Gil <lgil at ebi.ac.uk> on Tue, 26 Apr 2011 13:27:33 +0100:
> 
>> Hi Dario,
>> 
>> You can find all the ensembl data on the ftp: http://www.ensembl.org/info/data/ftp/index.html
>> 
>> The pig variations are stored here: ftp://ftp.ensembl.org/pub/release-62/variation/sus_scrofa/
>> The file that might interest you is Sus_scrofa.gvf.gz <ftp://ftp.ensembl.org/pub/release-62/variation/sus_scrofa/Sus_scrofa.gvf.gz>.
>> 
>> Cheers,
>> 
>> Laurent
>> 
>> 
>> On 25/04/2011 19:23, Dario Beraldi wrote:
>>> Hello,
>>> 
>>> I'm working with the Affymetrix Porcine chip (gene expression array for pig). I would like to download the position where each probe maps on the pig genome.
>>> 
>>> (I can see this information is present somewhere in ENSEMBL for example http://www.ensembl.org/Sus_scrofa/Location/Genome?db=core;fdb=funcgen;ftype=ProbeFeature;g=ENSSSCG00000014369;id=Ssc.4978.1.S1_at;ptype=pset;r=2:129356198-129357848;t=ENSSSCT00000015699 but I can't figure out how to extract the genome position in batch for all the probes).
>>> 
>>> Many thanks!
>>> 
>>> Dario
>>> 
>> 
> 
> 
> 
> -- 
> 
> Dr. Dario Beraldi
> Institute of Evolutionary Biology
> University of Edinburgh
> West Mains Road
> Edinburgh EH9 3JT
> Scotland, UK
> 
> 
> -- 
> The University of Edinburgh is a charitable body, registered in
> Scotland, with registration number SC005336.
> 
> 
> 
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Nathan Johnson
Senior Scientific Programmer
Ensembl Regulation
European Bioinformatics Institute
Wellcome Trust Genome Campus
Hinxton
Cambridge CB10 1SD

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